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DNACLUST specifications

Information


Unique identifier OMICS_01955
Name DNACLUST
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for DNACLUST

DNACLUST citations

 (20)
library_books

Centromere evolution and CpG methylation during vertebrate speciation

2017
Nat Commun
PMCID: 5705604
PMID: 29184138
DOI: 10.1038/s41467-017-01982-7

[…] Monomers in each chromosome of each strain separately were clustered using DNACLUST. From each cluster with >10 monomers, the longest monomer was selected as the representative. To calculate the alignment between a pair of two representative monomers, the similarity between […]

library_books

Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita

2017
Sci Rep
PMCID: 5601483
PMID: 28916791
DOI: 10.1038/s41598-017-11677-0

[…] were identified from the isotig gene models. In total, 84 and 95 genes with splicing variants were identified for mt− and mt+, respectively (Supplementary Tables  and ). Clustering analyses using the DNACLUST package were performed for the genes in the HMTS genomic regions in mt− and mt+; after manual correction of the clusters, they were classified into 46 and 67 clusters that were defined as spl […]

call_split

Taxa area relationship of aquatic fungi on deciduous leaves

2017
PLoS One
PMCID: 5515451
PMID: 28719634
DOI: 10.1371/journal.pone.0181545
call_split See protocol

[…] ucleotides below quality 20. Filtered reads were clustered with the Innovation Centre clustering algorithm. Briefly, reads were clustered at 100% identity and clustered/denoised at 99% identity using dnaclust (http://dnaclust.sourceforge.net/). Clusters with an abundance below 3 were discarded. Remaining clusters were scanned for chimeras with UCHIME denovo and UCHIME reference [] and clustered at […]

call_split

Deterministic versus stochastic model of reprogramming: new evidence from cellular barcoding technique

2017
Open Biol
PMCID: 5413903
PMID: 28446707
DOI: 10.1098/rsob.160311
call_split See protocol

[…] uality sequences (20% of the bases with quality values less than 20) and sequences with length less than 26 bp and more than 34 bp were discarded as well. The remaining sequences were clustered using DNAclust tool according to the similarity of barcode sequences []. For more details regarding clustering parameters, see §4.9 Barcoded library validation. Barcodes with only one copy number were elimi […]

call_split

Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage

2017
BMC Microbiol
PMCID: 5335695
PMID: 28253864
DOI: 10.1186/s12866-017-0947-0
call_split See protocol

[…] th of 250 bp and paired-end assembled using FLASH software []. Read counts per sample were checked to confirm no sample failed to be amplified or sequenced. Reads were clustered at 97% identity using DNACLUST [] and clusters showing abundances higher than 3 were then scanned for chimeras with UCHIME denovo and UCHIME reference in order to estimate final operational taxonomic units (OTUs) []. OTUs […]

call_split

Ecophylogeny of the endospheric root fungal microbiome of co occurring Agrostis stolonifera

2017
PeerJ
PMCID: 5466812
PMID: 28607843
DOI: 10.7717/peerj.3454
call_split See protocol

[…] Quality trimming and filtering of amplicons, OTU identification, and taxonomic assignments were carried out with a combination of publicly available sequencing data analysis tools (Cutadapt, Mothur, Dnaclust) and in-house python scripts within a Galaxy instance at the Genouest platform (http://www.genouest.org/), as described elsewhere (; ; ). Briefly, sequences shorter than 200 bp in length, wit […]

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DNACLUST institution(s)
Department of Computer Science, University of Maryland, College Park, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, MD, USA
DNACLUST funding source(s)
This work was supported by the National Institutes of Health [R01-HG-004885]; the National Science Foundation [IIS-0812111]; and the Bill and Melinda Gates Foundation.

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